Install efibootmgr:

sudo apt-get install efibootmgr

Then add to the kernel efi support

sudo modprobe efivars

Then run sudo efibootmgr to check your boot entries. It will return something like this:

BootCurrent: 0004
Timeout: 2 seconds
BootOrder: 2001,0003,0005,0006,0000
Boot0000* Lenovo Recovery System
Boot0001* EFI Network 0 for IPv6 (B8-88-E3-84-F3-EF)
Boot0002* EFI Network 0 for IPv4 (B8-88-E3-84-F3-EF)
Boot0003* Windows Boot Manager
Boot0004* EFI USB Device (SanDisk)
Boot0005* ubuntu
Boot2001* EFI USB Device

Then delete the option you dont want. In this example, Ubuntu is entry 5. the following could be called to delete entry 5 and remove it from the BootOrder.

(CAUTION: Before executing the following command make sure you enter the correct Boot entry number)

sudo efibootmgr -b 5 -B 

Further details described here: http://linux.die.net/man/8/efibootmgr

Note: as for anything that changes your bootloader, please ensure you have a good disk image that you can boot with.